Update app.py

app.py

@@ -23,7 +23,7 @@ print(moleculekit.__version__)
 
 def update(inp, file, mode, custom_resids, clustering_threshold):
     try:
-        pdb_file = file.name
+        filepath = file.name
     except:
         print("using pdbfile")
         try:
@@ -39,6 +39,7 @@ def update(inp, file, mode, custom_resids, clustering_threshold):
                     f"https://alphafold.ebi.ac.uk/files/AF-{pdb_file}-F1-model_v2.pdb",
                     f"files/{pdb_file}.pdb",
                 )
+            filepath = f"files/{pdb_file}.pdb"
         except AttributeError:
             if len(inp) == 4:
                 pdb_file = inp
@@ -46,17 +47,16 @@ def update(inp, file, mode, custom_resids, clustering_threshold):
                     f"http://files.rcsb.org/download/{pdb_file.lower()}.pdb1",
                     f"files/{pdb_file}.pdb",
                 )
+            filepath = f"files/{pdb_file}.pdb"
             else:
                 return "pdb code must be 4 letters or Uniprot code does not match", ""
 
     if mode == "All residues":
-        ids = get_all_protein_resids(
-            f"files/{pdb_file}.pdb",
-        )
+        ids = get_all_protein_resids(filepath)
     elif len(custom_resids)!=0:
         ids = [int(x) for x in custom_resids.split(',')]
     else:
-        ids = get_all_metalbinding_resids(f"files/{pdb_file}.pdb")
+        ids = get_all_metalbinding_resids(filepath)
     
     voxels, prot_centers, prot_N, prots = processStructures(pdb_file, ids)
     device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
@@ -94,7 +94,7 @@ def update(inp, file, mode, custom_resids, clustering_threshold):
     )
 
     return message, molecule(
-        f"files/{pdb_file}.pdb",
+        filepath,
         f"output/probes_{pdb_file}.pdb",
         f"output/metal_{pdb_file}.cube",
     )